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Author: Tim Booth <tbooth@ceh.ac.uk>
Description: Adapt path of some resources to Debian installation
--- a/ChimeraSlayer/ChimeraSlayer.pl
+++ b/ChimeraSlayer/ChimeraSlayer.pl
@@ -11,8 +11,8 @@
use CdbTools;
use File::Basename;
-my $db_NAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
-my $db_FASTA = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.fasta";
+my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
+my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
my $usage = <<_EOUSAGE_;
--- a/ChimeraSlayer/util/CS_add_taxonomy.pl
+++ b/ChimeraSlayer/util/CS_add_taxonomy.pl
@@ -13,7 +13,7 @@
my %acc_to_taxonomy;
{
- my $fasta_reader = new Fasta_reader("$FindBin::Bin/../../RESOURCES/rRNA16S.gold.fasta");
+ my $fasta_reader = new Fasta_reader("/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta");
while (my $seq_obj = $fasta_reader->next()) {
my $acc = $seq_obj->get_accession;
--- a/NAST-iEr/run_NAST-iEr.pl
+++ b/NAST-iEr/run_NAST-iEr.pl
@@ -12,8 +12,8 @@
use Nuc_translator;
-my $db_FASTA = "$FindBin::Bin/..//RESOURCES/rRNA16S.gold.fasta";
-my $db_NAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
+my $db_FASTA = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+my $db_NAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
my $usage = <<_EOUSAGE_;
--- a/WigeoN/run_WigeoN.pl
+++ b/WigeoN/run_WigeoN.pl
@@ -12,8 +12,8 @@
use CdbTools;
-my $refDB = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.fasta";
-my $refNAST = "$FindBin::Bin/../RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
+my $refDB = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.fasta";
+my $refNAST = "/usr/share/microbiomeutil-data/RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta";
my $usage = <<__EOUSAGE__;
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